Contacts of the strand formed by residues 338 - 345 (chain A) in PDB entry 5DVX
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLN 338 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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155A ALA* 5.2 1.6 - - + +
158A GLY* 3.4 4.1 - - - -
159A ARG 3.4 6.9 + - - -
160A PHE* 2.9 52.1 + - + +
161A GLN* 3.0 28.8 + - - +
267A GLY* 3.3 28.5 + - - +
268A ARG 4.5 0.2 - - - +
329A GLY 3.4 5.8 - - - +
330A SER* 4.0 0.9 - - - -
336A CYS 3.5 0.9 + - - +
337A ALA* 1.3 75.4 - - - +
339A GLY* 1.3 65.1 + - - +
340A VAL* 3.3 4.6 + - - +
406A CL 3.4 22.9 - - - +
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Residues in contact with GLY 339 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267A GLY 4.8 1.1 - - - -
268A ARG 3.5 4.9 - - - +
269A PRO* 3.9 14.4 - - - -
270A GLY* 2.8 29.3 + - - -
271A GLY 4.0 1.6 + - - -
272A LEU 4.7 0.8 + - - -
328A GLU* 3.4 26.5 + - - +
329A GLY 3.0 4.4 + - - -
338A GLN* 1.3 79.2 - - - +
340A VAL* 1.3 61.3 + - - +
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Residues in contact with VAL 340 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267A GLY 6.3 0.2 - - - +
272A LEU* 3.5 26.7 - - + +
274A VAL* 3.9 23.6 - - + -
328A GLU* 3.4 3.9 - - - -
329A GLY 2.8 35.4 + - - +
330A SER 3.8 0.9 - - - +
331A LEU* 3.7 24.5 - - + +
337A ALA* 3.6 22.4 - - + +
338A GLN 4.3 2.5 - - - +
339A GLY* 1.3 78.9 - - - +
341A ILE* 1.3 66.9 + - - +
342A TRP* 3.5 25.4 + - + +
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Residues in contact with ILE 341 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214A LEU* 3.7 19.7 - - + -
218A ARG* 4.1 20.9 - - - +
220A TYR* 3.2 24.0 - - + +
270A GLY* 3.8 20.2 - - - +
272A LEU 3.0 9.8 + - - +
273A ALA* 3.3 7.8 - - + +
274A VAL 2.9 26.6 + - - +
326A GLN* 4.0 17.9 - - + +
327A TYR 3.8 3.6 - - - +
328A GLU* 4.8 2.7 - - + +
339A GLY 4.5 1.1 - - - +
340A VAL* 1.3 71.6 - - - +
342A TRP* 1.3 62.5 + - - +
343A THR* 4.8 0.7 + - - -
404A GOL 3.8 31.2 - - - +
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Residues in contact with TRP 342 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162A SER* 3.1 18.1 + - - -
239A HIS* 3.6 19.5 - + - -
251A HIS* 3.6 38.8 - + - -
274A VAL* 3.4 43.1 - - + -
276A ALA* 4.1 10.8 - - + -
326A GLN* 3.2 9.4 - - - +
327A TYR* 2.9 57.1 + - + +
329A GLY 4.0 5.4 - - - -
330A SER 2.8 29.9 + - - +
331A LEU* 4.8 2.0 - - + -
332A THR* 3.7 20.2 - - + -
340A VAL* 3.5 25.7 - - + +
341A ILE* 1.3 73.0 - - - +
343A THR* 1.3 60.1 + - - +
344A VAL* 4.2 1.8 - - + -
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Residues in contact with THR 343 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180A LEU* 4.1 13.0 - - + -
214A LEU* 3.7 12.6 - - - +
274A VAL 3.0 7.3 + - - +
275A LEU* 3.6 24.2 - - + +
276A ALA* 2.9 27.5 + - - +
324A TYR* 3.6 36.1 - - + -
325A PHE 3.3 3.1 - - - -
326A GLN* 2.9 23.3 + - - +
341A ILE* 4.5 0.7 + - - +
342A TRP* 1.3 72.9 - - - +
344A VAL* 1.3 63.9 + - - +
345A PHE* 4.1 2.5 + - + +
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Residues in contact with VAL 344 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166A ILE* 3.9 27.1 - - + -
239A HIS* 4.2 22.0 - - + +
249A GLU* 5.8 0.4 - - - +
276A ALA* 3.4 22.0 - - + +
277A ALA* 5.4 0.7 - - - -
278A PHE* 3.9 26.9 - - + -
324A TYR* 3.4 2.6 - - - -
325A PHE* 2.8 45.8 + - + +
327A TYR* 4.7 10.8 - - + -
342A TRP* 5.0 1.1 - - + -
343A THR* 1.3 76.4 - - - +
345A PHE* 1.3 74.0 + - - +
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Residues in contact with PHE 345 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180A LEU* 4.0 24.7 - - + -
182A LEU* 6.3 0.2 - - + -
275A LEU* 4.5 18.8 - - + -
276A ALA 3.0 30.8 + - - +
277A ALA* 4.0 5.6 - - + -
278A PHE* 4.6 10.7 - - - -
317A LEU* 4.4 21.8 - - + -
318A PRO* 3.7 29.8 - - + -
320A ASP 3.4 18.2 - - - -
321A PHE* 3.6 37.7 - + - -
323A ARG 4.1 4.9 - - - -
324A TYR* 4.2 4.7 - - + -
325A PHE* 4.8 1.2 - - - -
343A THR* 5.0 2.5 - - + -
344A VAL* 1.3 82.9 - - - +
346A ASN* 1.3 63.4 + - - +
347A GLN 3.4 19.6 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il